Variant report

Variant	rs471462
Chromosome Location	chr11:74515470-74515471
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:74510779..74512566-chr11:74514650..74516434,2	K562	blood:
2	chr10:2026960..2027790-chr11:74514864..74515669,2	MCF-7	breast:
3	chr11:74458997..74460501-chr11:74513835..74516605,2	MCF-7	breast:
4	chr11:74510779..74513147-chr11:74514555..74516434,3	K562	blood:
5	chr11:74514487..74517176-chr11:74519727..74521756,2	MCF-7	breast:
6	chr11:74514568..74516629-chr11:74518036..74519689,2	MCF-7	breast:
7	chr11:74514839..74517233-chr11:74520052..74522234,2	K562	blood:

Variant related genes	Relation type
ENSG00000166439	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs11236269	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs11605604	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12363224	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1282460	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1282461	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs1282689	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1282690	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1282692	0.96[CEU][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.87[EUR][1000 genomes]
rs1292895	0.96[CEU][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1297319	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1303525	0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1315297	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1583342	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.87[LWK][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2028343	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2028344	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2033532	0.86[ASW][hapmap];0.96[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.98[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2919057	1.00[JPT][hapmap]
rs41531051	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs473080	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs473256	0.86[ASW][hapmap];0.96[CEU][hapmap];0.93[CHB][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs480840	1.00[ASW][hapmap];0.84[CEU][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.85[MKK][hapmap];0.85[YRI][hapmap];0.87[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs483615	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4944945	0.85[YRI][hapmap]
rs495246	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs497772	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs502225	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs505688	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.96[MKK][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs508319	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs511021	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs511890	0.96[CEU][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.88[EUR][1000 genomes]
rs512780	1.00[ASW][hapmap];0.88[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.93[JPT][hapmap];0.82[LWK][hapmap];0.85[MKK][hapmap];0.85[YRI][hapmap];0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs513137	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs519741	1.00[ASW][hapmap];0.96[CEU][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.92[MKK][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs527529	0.88[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs529249	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs529488	0.86[ASW][hapmap];0.96[CEU][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs537054	0.96[CEU][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.87[EUR][1000 genomes]
rs538502	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs543244	1.00[ASW][hapmap];0.96[CEU][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.92[MKK][hapmap];0.98[TSI][hapmap];0.85[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs546643	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs550491	1.00[CHB][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs550869	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs550980	0.82[CEU][hapmap];0.87[CHB][hapmap];0.85[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes]
rs557483	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs561589	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.99[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs562265	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs565767	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs567956	1.00[ASW][hapmap];0.96[CEU][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs568558	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs568758	0.92[CEU][hapmap];0.86[CHB][hapmap];0.92[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs571446	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs573925	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs577063	0.82[EUR][1000 genomes]
rs577102	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs580142	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs590105	1.00[CEU][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs599722	1.00[ASW][hapmap];0.96[CEU][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.92[MKK][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs603062	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs614832	0.96[CEU][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs616085	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs624786	0.81[ASW][hapmap];0.96[CEU][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs625268	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs629573	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs641584	1.00[CEU][hapmap];0.93[CHB][hapmap];0.85[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs643807	1.00[ASW][hapmap];0.84[CEU][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.96[MKK][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs646287	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs688665	0.92[CEU][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9444	0.92[ASW][hapmap];0.96[CEU][hapmap];0.86[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.87[LWK][hapmap];0.85[MKK][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs997465	0.93[ASW][hapmap];0.94[JPT][hapmap];0.92[MKK][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757451	chr11:73842609-74545888	Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	esv2759837	chr11:73842609-74557597	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
3	esv34979	chr11:73878688-74533452	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
4	esv2758277	chr11:73887567-74557597	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
5	nsv825994	chr11:73936667-74534455	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
6	nsv932190	chr11:74359867-74618935	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	41 gene(s)	inside rSNPs	diseases
7	nsv897916	chr11:74465068-74574677	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv897917	chr11:74474266-74595507	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs471462	XRRA1	cis	Muscle Skeletal	GTEx
rs471462	RNF169	cis	lymphoblastoid	seeQTL
rs471462	XRRA1	cis	Whole Blood	GTEx
rs471462	XRRA1	cis	Thyroid	GTEx
rs471462	XRRA1	cis	Esophagus Mucosa	GTEx
rs471462	XRRA1	cis	Adipose Subcutaneous	GTEx
rs471462	XRRA1	cis	Artery Tibial	GTEx
rs471462	XRRA1	cis	lymphoblastoid	seeQTL
rs471462	RP11-147I3.1	cis	Thyroid	GTEx
rs471462	XRRA1	Cis_1M	lymphoblastoid	RTeQTL
rs471462	XRRA1	cis	lung	GTEx

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:74494800-74530600	Weak transcription	NH-A	brain
2	chr11:74496000-74518200	Weak transcription	Psoas Muscle	Psoas
3	chr11:74496200-74533000	Weak transcription	Fetal Brain Male	brain
4	chr11:74502600-74519400	Weak transcription	HUVEC	blood vessel
5	chr11:74502600-74527800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr11:74502800-74545600	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr11:74503000-74519600	Weak transcription	Aorta	Aorta
8	chr11:74503000-74522600	Weak transcription	NHLF	lung
9	chr11:74503000-74528400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr11:74503000-74529400	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr11:74503000-74530200	Weak transcription	Rectal Smooth Muscle	rectum
12	chr11:74503000-74530600	Weak transcription	HSMMtube	muscle
13	chr11:74503000-74531600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr11:74503000-74533000	Weak transcription	Right Ventricle	heart
15	chr11:74503200-74519400	Weak transcription	Brain Hippocampus Middle	brain
16	chr11:74503200-74519600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr11:74503200-74524800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr11:74503200-74528600	Weak transcription	Lung	lung
19	chr11:74503200-74533000	Weak transcription	Gastric	stomach
20	chr11:74503200-74537800	Weak transcription	Pancreas	Pancrea
21	chr11:74503800-74529000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr11:74504000-74522200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr11:74504200-74516800	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr11:74504200-74518000	Weak transcription	Brain Cingulate Gyrus	brain
25	chr11:74504200-74518200	Weak transcription	Colon Smooth Muscle	Colon
26	chr11:74504200-74519000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr11:74504200-74519200	Weak transcription	Fetal Brain Female	brain
28	chr11:74504200-74519400	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr11:74504200-74528600	Weak transcription	Stomach Smooth Muscle	stomach
30	chr11:74504400-74516800	Weak transcription	A549	lung
31	chr11:74504400-74522000	Weak transcription	Primary T cells fromperipheralblood	blood
32	chr11:74504400-74522800	Weak transcription	Duodenum Mucosa	Duodenum
33	chr11:74504400-74531600	Weak transcription	HMEC	breast
34	chr11:74504400-74534600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr11:74504600-74519400	Weak transcription	Brain Substantia Nigra	brain
36	chr11:74504600-74523200	Weak transcription	Hela-S3	cervix
37	chr11:74505400-74519400	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr11:74505400-74520800	Weak transcription	NHDF-Ad	bronchial
39	chr11:74505400-74521200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr11:74505400-74521200	Weak transcription	HSMM	muscle
41	chr11:74505400-74527600	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr11:74505600-74519400	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr11:74505800-74519600	Weak transcription	Fetal Kidney	kidney
44	chr11:74505800-74521200	Weak transcription	Osteobl	bone
45	chr11:74506000-74521400	Weak transcription	HepG2	liver
46	chr11:74506200-74523800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr11:74506600-74521800	Weak transcription	Adipose Nuclei	Adipose
48	chr11:74506600-74522000	Weak transcription	Fetal Thymus	thymus
49	chr11:74506600-74522400	Weak transcription	Liver	Liver
50	chr11:74507000-74530200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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